I think Mk should go to Ubers because of the bans of Mgen and MBlaz. I will use a 5th gen analogy to portray my argument.
For those of you who were around when the new Tornadus was introduced in 5th gen OU, it was very controversial. It had speed, bulk, ability, and the move-pool to be successful, so much so that it was banned to Ubers. As a result of this, Pokemon such as Breloom and Keldeo became even more rampant. Now, I am not saying Breloom and Keldeo were not good before the banning of Torn; however, it is undeniable that because Torn was banned, the usage and effectiveness of both Breloom and Keldeo increased drastically. Keldeo, specifically, got suspect tested since it could run a variety of powerful sets, such as Scarfed, Expert Belt, or Specs. People were on the fence, because Rain Boosted Specs Hydro-Pumps hurt many pokes, even those who resist it (think specially defensive Celebi), but it didn't seem to be entirely meta-game changing.
Because Tornadus was around when Keldeo was first introduced, Keldeo could not run an effective Calm Mind Set, Expert Belt, or Specs. Because Keldeo was often paired up with Politoed, it gave Torn free reign to spamming LO Hurricanes. It would easily outspeed Keldeo (barring scarfed), and knock it out, force it out, or check setting up Keldeos with Hurricane. With Tornadus gone, a huge check to Keldeo was locked away in ubers.
In today's meta, Mk could be dealt with Mblaz (resist sucker punch, outspeeds after +1) and Mgar. Mgar wasn't that great to beat Mkan (I think the standard Sub-Disable does better at it), but Mblaz could destroy most Khan, thereby people using it less and less. Now, because of the banning of two great Megas, and arguably better, Khan is now the flag-ship Mega-Mon for 6th Gen OU. Because of this, I feel that Mkhan should be illegal in the OU tier.
Mkhan now lacks an offensive check, barring Terrakion and Keldeo (Cob and Virizion do not have a popular niche in OU). Because of this, Mkhan has an easier time sweeping teams. If your team lacks SubDisable Gengar, Rocky Helmet Ferrothorn or Chomp, or Sableye, you will struggle playing around Mkhan. I am not saying that these pokes are bad, because honestly, they are good in standard meta; however, with the prevalence of Mkhan being around, it makes these sets more appealing to use for players that struggle with Mkhan, thereby shifting the Meta (Having to use Sableye specifically to check Khan isn't healthy...it's like using Claydol to check Terrak).
It has great bulk for an offensive mon. It is unlikely to be OHKd by any Non-SE STAB, even from beasts like Lando and the likes. It has a competitive speed tier, just out-speeding Genesect, and speed tying Jirachi. For those who do outspeed Khan, it can be easily defeated using Sucker Punch.
It has a great movepool. PuP is essentially a weaker brick break + SD that can only be blocked via protecting moves and ghost types. Earthquake allows one to deal with Aegislash, Steel Types, and overall has good neutral coverage. Normal is a great offensive typing, being resisted by Rock and Steel, only to be defeated by EQ. Sucker Punch/Crunch allows you to hit ghost types.
It's ability allows one to essentially ignore substitute, have a higher crit ratio, and essentially make focus sash and sturdy useless. That is all I have to say for now. Please feel free to critique.
I am writing this at 4:21am when I should be studying for finals, so please bear with my bad grammar and lack of organization. Thanks!